[phenixbb] protein atom selection

[wtempel]

Hello Nigel,
phenix.fetch_pdb 4yz8; phenix.pdbtools 4yz8.pdb keep="(protein)"
modify.output.file_name=4yz8-protein.pdb stop_for_unknowns=False
Might the actual presence of a peptide bond (in the same chain, at least)
be a reasonable requirement?
W.
​

On Fri, Feb 3, 2017 at 3:01 PM, Nigel Moriarty <nwmoriarty at lbl.gov> wrote:

> Wolfram
>
> I can understand your surprise. I believe it's because the Monomer Library
> contradicts the Chemical Components and calls SAM an L-peptide. Can you
> describe how you are selecting so I can debug easily.
>
> Cheers
>
> Nigel
>
> ---
> Nigel W. Moriarty
> Building 33R0349, Molecular Biophysics and Integrated Bioimaging
> Lawrence Berkeley National Laboratory
> Berkeley, CA 94720-8235
> Phone : 510-486-5709 <(510)%20486-5709>     Email : NWMoriarty at LBL.gov
> Fax   : 510-486-5909 <(510)%20486-5909>       Web  : CCI.LBL.gov
>
> On Fri, Feb 3, 2017 at 11:42 AM, wtempel <wtempel at gmail.com> wrote:
>
>> Hello all,
>> in my hands and to my surprise, PHENIX atom selections such as "protein"
>> or "peptide" would include a co-factor like SAM. Did others notice that
>> also? Is this behavior what most users would want or even expect?
>> Best regards.
>> Wolfram Tempel
>>
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>
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